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{
"code": "SASDVF9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Allergen-induced structural rearrangements in IgE: insights from SAXS and molecular dynamics.",
"publication": {
"title": "Allergen-induced structural rearrangements in IgE: insights from SAXS and molecular dynamics.",
"author_list": "Gómez-Velasco H, García-Ramírez B, Siliqi D, Graewert MA, Quintero-Martinez A, Ortega E, Rodríguez-Romero A",
"journal": "Int J Biol Macromol",
"doi": "10.1016/j.ijbiomac.2025.147658",
"pmid": "40953619",
"published_date": "2025 Sep 13"
},
"status": "released",
"submitted_date": "2025-05-07",
"released_date": "2025-09-17"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVF9.dat",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVF9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVF9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVF9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Murine Immunoglobulin E (IgE) antibodies",
"short_name": "IgE",
"sequence": "EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRTKTNNYVTYYADSVKDRFTISRDDSQSM\r\nLYLQMNNLKTEDTAMYYCVRHVGDYWGQGTSVTVSSASIRNPQLYPLKPCKSMTLGCLVKDYFPGPVTVTWYSDSLNMST\r\nVNFPALGSELKVTTSQVTSWGKSAKNFTCHVTHPPSFNESRTILVRPVNITEPTLELLHSSCDPNAFHSTIQLYCFIYGH\r\nILNDVSVSWLMDDREITDTLAQTVLIKEEGKLASTCSKLNITEQQWMSESTFTCKVTSQGVDYLAHTRRCPDHEPRGVIT\r\nYLIPPSPLDLYQNGAPKLTCLVVDLESEKNVNVTWNQEKKTSVSASQWYTKHHNNATTSITSILPVVAKDWIEGYGYQCI\r\nVDHPDFPKPIVRSITKTPGQRSAPEVYVFPPPEEESEDKRTLTCLIQNFFPEDISVQWLGDGKLISNSQHSTTTPLKSNG\r\nSNQGFFIFSRLEVAKTLWTQRKQFTCQVIHEALQKPRKLEKTISTS\r\nDIQMTQSPASLSASVGETVTITCRASGNIHNYLAWFQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQP\r\nEDFGSYYCQHFWSTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVL\r\nNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE\r\n\r\nEVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRTKTNNYVTYYADSVKDRFTISRDDSQSM\r\nLYLQMNNLKTEDTAMYYCVRHVGDYWGQGTSVTVSSASIRNPQLYPLKPCKSMTLGCLVKDYFPGPVTVTWYSDSLNMST\r\nVNFPALGSELKVTTSQVTSWGKSAKNFTCHVTHPPSFNESRTILVRPVNITEPTLELLHSSCDPNAFHSTIQLYCFIYGH\r\nILNDVSVSWLMDDREITDTLAQTVLIKEEGKLASTCSKLNITEQQWMSESTFTCKVTSQGVDYLAHTRRCPDHEPRGVIT\r\nYLIPPSPLDLYQNGAPKLTCLVVDLESEKNVNVTWNQEKKTSVSASQWYTKHHNNATTSITSILPVVAKDWIEGYGYQCI\r\nVDHPDFPKPIVRSITKTPGQRSAPEVYVFPPPEEESEDKRTLTCLIQNFFPEDISVQWLGDGKLISNSQHSTTTPLKSNG\r\nSNQGFFIFSRLEVAKTLWTQRKQFTCQVIHEALQKPRKLEKTISTSL\r\n\r\nDIQMTQSPASLSASVGETVTITCRASGNIHNYLAWFQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQP\r\nEDFGSYYCQHFWSTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVL\r\nNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE",
"organism": "Mus musculus",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "",
"mw": 165.383,
"total_mw": 165.383,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The molecular weight of a murine IgE, considering glycosylations, is approximately 190-198 kDa (protein 180 kDa + 10-18 kDa glycosylation). This is a rough estimate; the actual molecular weight can vary depending on the specific glycosylation patterns and modifications of the IgE molecule."
},
{
"long_name": "Profilin-2",
"short_name": "PRF",
"sequence": "MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSDDDDKMSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTLAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVERLGDYLIDQGY",
"organism": "Hevea brasiliensis",
"uniprot_code": "Q9STB6",
"uniprot_range_first": 1,
"uniprot_range_last": 131,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSWQAYVDDHLMCEIEGNHLSAAAIIGQDGSVWAQSANFPQFKSEEITGIMSDFHEPGTL\nAPTGLYIGGTKYMVIQGEPGAVIRGKKGPGGVTVKKTNQALIIGIYDEPMTPGQCNMIVE\nRLGDYLIDQGY",
"mw": 18.283,
"total_mw": 18.283,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Allergen Hev b 8 protein (profilin). The protein construct contains an additional 39 non-native amino acids at the N-terminus (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSDDDDK)."
}
],
"buffer": {
"name": "20 mM Tris, 50 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.4,
"deuteration": null
},
"purity_method": null,
"name": "Mouse complex murine Immunoglobulin E (IgE) antibody with profilin",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Bari, Italy",
"full_name": "CNR - Institute of Crystallography, Bari, Italy",
"webpage": "http://www.ba.ic.cnr.it"
}
],
"contributor_name": "Dritan",
"contributor_surname": "Siliqi",
"orcid": "https://orcid.org/0000-0003-1415-8725"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-10-03",
"storage_temperature": 4.0,
"cell_temperature": 15.0,
"exposure_time": 3.0,
"number_of_frames": 620,
"wavelength": 0.094,
"sample_detector_distance": 3.7,
"concentration_min": null,
"concentration_max": 5.8,
"sample_volume": 50.0,
"flow_rate": 0.07,
"s_min": 0.045,
"s_max": 3.4,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVF9_fit1_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVF9_fit1_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/dammifs_CXHw1IP.log",
"symmetry": "P1",
"comment": null,
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVF9_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.184,
"p_value": 0.0284,
"fit_residual_plot": "SASDVF9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVF9_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammifs_EFFpt3K.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVF9_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "7sbd",
"ext_code": "7SBD",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVF9_fit2_model1.pdb",
"model_mw": 186.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVF9_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 2.332,
"p_value": 0.0,
"fit_residual_plot": "SASDVF9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVF9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cp96_IgE_PRF_1.log",
"software_version": "3.2.1",
"description": "The construct IgE-PROFILIN fitting the experimental data"
}
],
"estimated_volume_method": null,
"pddf_software": "ScÅtter",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "Synchrotron SAXS data from solutions of allergen Hev b 8 bound to murine IgE in 20 mM Tris, 50 mM NaCl, pH 8.4 were collected on the B21 beamline at Diamond (Didcot, UK) using an EigerX 4M-Detrics detector at a sample-detector distance of 3.7 m and the wavelength of 0.95 A. In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 70.00 μl sample at 6.2 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 15°C. 620 successive 3 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.\r\nThe molecular weight of a murine IgE, considering glycosylation, is approximately 190-198 kDa (protein 180 kDa + 10-18 kDa glycosylation). This estimate is an approximation; the actual molecular weight can vary depending on the specific glycosylation patterns and modifications of the IgE molecule. In this way the estimated MW for the complex (including the the Profilin with his TAG) is approximately 240 kDa.",
"experiment_description": null,
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 240.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 220.0,
"porod_mw_error": null,
"pddf_i0": 0.7227735,
"pddf_i0_error": null,
"guinier_i0": 0.101458,
"guinier_i0_error": null,
"pddf_rg": 6.07,
"pddf_rg_error": null,
"guinier_rg": 6.034,
"guinier_rg_error": 0.139,
"pddf_dmax": 19.9,
"pddf_dmax_error": null,
"porod_volume": 504.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 32,
"guinier_point_last": 131,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVF9_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-09-17T10:12:43.181060+02:00",
"bragg_peak": []
}
